Enrichment tests are based on the well-established globaltest to test associations between metabolite sets and the outcome. The algorithm uses a generalized linear model to compute a ‘Q-stat’ for each metabolite set. The Q-stat is calculated as the average of the Q values calculated for the each single metabolites; while the Q value is the squared covariance between the metabolite and the outcome. The globaltest has been shown to exhibit similar or superior performance when tested against several other popular methods.
Metabolite sets: Unlike transcriptomics which allows comprehensive gene expression profiling, targeted metabolomics usually covers only a small percentage of metabolome (the actual coverage is platform/protocol specific). This means that metabolites (defined in our current pathways or metabolite sets) do not have equal probabilities of being measured in your studies, and the enriched functions are the results from both platform/protocol specific effects and biological perturbations. Since the primary interest is to detect the latter, we highly recommend uploading a reference metabolome containing all measurable metabolites from your platform to eliminate the former effects.
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